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Determining minimum energy conformations of polypeptides by dynamic programming.

S Vajda1, C Delisi

  • 1Department of Biomathematical Sciences, Mount Sinai School of Medicine, New York, New York 10029.

Biopolymers
|December 1, 1990
PubMed
Summary
This summary is machine-generated.

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This study introduces a combinatorial optimization method for finding polypeptide low-energy conformations. A version with limited local minimization successfully identified conformations for all tested peptides, offering speed advantages.

Area of Science:

  • Computational chemistry
  • Biophysics
  • Protein structure prediction

Background:

  • Determining low-energy conformations of short polypeptides is crucial for understanding protein folding and function.
  • The multiple-minima problem presents a significant challenge in conformational searching.

Purpose of the Study:

  • To develop and evaluate a combinatorial optimization approach for efficiently solving the multiple-minima problem in polypeptide conformation determination.
  • To compare the performance of a purely discrete search with a hybrid approach incorporating limited continuous local minimization.

Main Methods:

  • A generalized dynamic programming algorithm was employed, representing each residue by discrete states.
  • Two procedures were implemented: a fully discrete search followed by refinement, and a combinatorial search with limited local minimization.

Related Experiment Videos

  • The methods were tested on 17 short peptides using a consistent potential energy function.

    • Main Results:

    • The purely discrete method was very fast but successful in only 14 out of 17 cases.
    • The approach with limited local minimization accurately found conformations for all 17 peptides, often with lower energies than previously reported.
    • Results were largely independent of the cutoff energy parameter.

    Conclusions:

    • The combinatorial optimization approach, particularly with limited local minimization, provides an efficient and effective method for determining low-energy polypeptide conformations.
    • This method offers significant speed advantages over other global minimization techniques while maintaining high accuracy.